If you already had a save file for this game and the file for the save file was actually deleted from the 3DS SD Card you can try using Recuva ( http://www.piriform.com/recuva ) to restore it.

But if you tried to run the game again and it said "save corrupted, formatting save file" or something along those lines, it's improbable that you can recover it (unless if gateway actually deletes the save file on the SD card and create a new one instead of overwriting it).

The save games save onto your SD card, so chances are you never actually properly saved the game or else they would still be there.... or did they get corrupted when you ejected the card during saving?

The multirom takes the save from the SD and plays with it.
When you save, it updates the save in the mSD at the moment.
When you shutdown or home+x, the save transfers back to the SD.

If you eject by accident, you should immediately put the red card mSD in a computer and see if the updated save is still there.
Launching the game after an eject will simply reload the SD save, deleting the updated save on the mSD.